Structure of deviations from optimality in biological systems

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 48, 2009, Pages 20544-20549

  Pérez Escudero, Alfonso ^a,b,c   Rivera Alba, Marta ^a,b   De Polavieja, Gonzalo G ^a,b  

^a INSTITUTO CAJAL   (Spain)

^b INSTITUTO NICOLÁS CABRERA   (Spain)

^c INSTITUTO DE ÓPTICA   (Spain)

Author keywords

Caenorhabditis elegans; Escherichia coli; Evolution; Neuroanatomy; Optimization

Indexed keywords

ANIMAL BEHAVIOR; ANIMAL EXPERIMENT; ARTICLE; BIOMASS PRODUCTION; CAENORHABDITIS ELEGANS; COST; ESCHERICHIA COLI; EVOLUTION; GROWTH RATE; MICROBIAL BIOMASS; MOLECULAR BIOLOGY; NERVE CELL; NEUROANATOMY; NONHUMAN; OPTIMISM; PRIORITY JOURNAL; PROBABILITY;

ADAPTATION, BIOLOGICAL; ANIMALS; BAYES THEOREM; CAENORHABDITIS ELEGANS; COMPUTER SIMULATION; ENERGY METABOLISM; ESCHERICHIA COLI; EVOLUTION; MODELS, BIOLOGICAL; NEURAL PATHWAYS; SYSTEMS BIOLOGY;

ANIMALIA; CAENORHABDITIS ELEGANS; ESCHERICHIA COLI;

EID: 73949153189     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0905336106     Document Type: Article

References (42)

1. Barton NH, Briggs DEG, Eisen JA, Goldstein DB, Patel NH (2007) Evolution (Cold Spring Harbor Lab Press, Cold Spring Harbor, NY).
2. Alexander RM (1996) Optima for Animals (Princeton Univ Press, Princeton).
3. Parker GA, Maynard Smith J (1990) Optimality theory in evolutionary biology. Nature 348:27-33.
4. Freeland SJ, Hurst LD (1998) The genetic code is one in amillion. J Mol Evol 47:238-248.
5. Itzkovitz S, Alon U (2007) The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res 17:405-412.
6. Dekel E, Alon U (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature 430:588-592.
7. Tkacik G, Callan CG, Jr, Bialek W (2008) Information flow and optimization in transcriptional regulation. Proc Natl Acad Sci USA 105:12265-12270.
8. Palsson BO (2006) Systems Biology: Properties of Reconstructed Networks (Cambridge Univ Press, Cambridge, UK).
9. Varma A, Palsson BO (1994) Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3010. Appl Environ Microbiol 60:3724-3730.
10. Edwards JS, Ibarra RU, Palsson BO (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19:125-130.
11. Ibarra RU, Edwards JS, Palsson BO (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420:186-189.
12. Segre D, Vitkup D, Church GM (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 99:15112-15117.
13. Schuetz R, Kuepfer L, Sauer U (2007) Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol 3:119-133.
14. Chklovskii DB, Schikorski T, Stevens CF (2002) Wiring optimization in cortical circuits. Neuron 34:341-347.
15. Klyachko VA, Stevens CF (2003) Connectivity optimization and the positioning of cortical areas. Proc Natl Acad Sci USA 100:7937-7941.
16. Buzsaki G, Geiler C, Henze DA, Wang X-J (2004) Interneuron diversity series: Circuit complexity and axon wiring economy of cortical circuits. Trends Neurosci 27:186-193.
17. Chklovskii DB (2004) Exact solution for the optimal neuronal layout problem. Neural Comput 16:2067-2078.
18. Chen BL, Hall DH, Chklovskii DB (2006) Wiring optimization can relate neuronal structure and function. Proc Natl Acad Sci USA 103:4723-4728.
19. Ahn Y-Y, Jeong H, Kim BJ, (2006) Wiring cost in the organization of a biological neuronal network. Physica A 367:430-537.
20. Kaiser M, Hiltetag CC (2006) Nonoptimal component placement, but short processing paths, due to long-distance projections in neural systems. PloS Comp Biol 2:e95.
21. Perez-Escudero A, de Polavieja G (2007) Optimally wired subnetwork determines neuronanatomy of Caenorhabditis elegans. Proc Natl Acad Sci USA 104:17180-17185.
22. Laughlin SB (1981) A simple coding procedure enhances a neuron's information capacity. Z Naturforsch 36c:910-912.
23. Rieke F, Warland D, Bialek W (1993) Coding efficiency and information rates in sensory neurons. Europhys Lett 22:151-156.
24. de Polavieja GG (2002) Errors drive the evolution of biological signalling to costly codes. J Theor Biol 214:657-664.
25. Oaten A (1977) Optimal foraging in patches: a case for stochasticity. Theor Pop Biol 12: 263-285'
26. Murray CD (1926) The physiological principle of minimum work. I. The vascular system and the cost of blood volume. Proc Natl Acad Sci USA 12:207-214.
27. Murray CD (1926) The physiological principle of minimum work applied to the angle branching of arteries. J Gen Physiol 9:235-841.
28. Weibel ER, Gomez DM (1962) Architecture of the human lung. Science 137:577-585.
29. Sherman TF (1981) On connecting large vessels to small. J Gen Physiol 78:431-453.
30. Gould SJ, Lewontin RC (1979) The spandrels of San Marco and the panglosian paradigm: A critique of the adaptationist program. Proc R Soc London Ser B 205:581-598.
31. Lynch M, Walsh B (1998) Genetics and Analysis of Quantitative Traits (Sinauer, Sunderland, MA).
32. Michalewicz Z, Fogel DB (2000) How to Solve It: Modern Heuristics (Springer, New York).
33. Kirkpatrick S, Gelatt CD, Vecchi MP (1983) Optimization by simulated annealing. Science 220:671-680.
34. White JG, Southgate E, Thomson JN, Brenner S (1986) The structure of the nervous system of the nematode Caenorhabditis elegans. Philos Trans R Soc London Ser B 314:1-340.
35. Hall DH, Russell RL (1991) The posterior nervous system of the nematode Caenorhabditis elegans: Serial reconstruction of identified neurons and complete pattern of synaptic interactions. J Neurosci 11:1-22.
36. Becker SA, et al. (2007) Quantitative prediction of cellular metabolism with constraintbased models: the COBRA toolbox. Nat Protocols 2:727-738.
37. Nanchen A, Schicker A, Sauer U (2006) Nonlinear dependency of intracellular fluxes on growth rate in miniaturized continuous cultures of Escherichia coli. Appl Environ Microbiol 72:1164-1172.
38. Haldi J, Whitcomb D (1967) Economies of scale in industrial plants. J Polit Econ 75:373-385.
39. Nerlove M (1963) Returns to scale in electricity supply. Measurement in Economics, eds Christ F, et al (Stanford Univ Press, Stanford, CA), pp 167-198.
40. Christensen LR, Greene WH (1976) Economies of scale in U.S. electric power generation. J Polit 4:655-676.
41. Janic M (2007) Modelling the full costs of an intermodal and road freight transport network. Transportation Res D 12:33-44.
42. McCann P (2001) A proof of the relationship between optimal vehicle size, haulage length and structure of distance-transport costs. Transportation Res A 35:671-693.